Program: 18. Cancer Associated Fibroblast: Inflammatory.

Stromal 2 (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for Stroma subcluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.49e-05
Mean rank of genes in gene set: 2034.25
Rank on gene expression program of genes in gene set:

Subepicardial mesenchyme (Kameneva)
Marker gene were obtained from Fig. 1D of Kameneva et al (PMID 33833454). These genes were used by the authors to annotate each cell type in their human fetal adrenal scRNA-seq data obtained 6, 8, 9, 11, 12 and 14 weeks post conception.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.15e-05
Mean rank of genes in gene set: 797.14
Rank on gene expression program of genes in gene set:

Stress response (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.06e-04
Mean rank of genes in gene set: 724.8
Rank on gene expression program of genes in gene set:

Mesenchymal (Olsen)
Markers listed in on page 3 of the main text of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - these markers are stated as being expressed in a group of mesenchymal-like cells (some at least claimed to be neuroblastoma cells) shown in their UMAP representation on Fig. 1D. They reference the two Nature Genetics paper.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.44e-04
Mean rank of genes in gene set: 127
Rank on gene expression program of genes in gene set:

Mesenchymal cells (Yuan)
Obtained from Fig. 1 of Yuan et al. https://www.biorxiv.org/content/10.1101/2020.05.15.097469v1:
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.80e-04
Mean rank of genes in gene set: 391.5
Rank on gene expression program of genes in gene set:

Stroma (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for the broad Stroma cluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 6.89e-04
Mean rank of genes in gene set: 1092.8
Rank on gene expression program of genes in gene set:

Stress response (Dong)
Markers obtained in computationally inferred meta program (by NMF applied to their neuroblastoma sc-RNA-seq data) from Fig. 5(a) of Dong et al. (PMID 32946775).:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.36e-03
Mean rank of genes in gene set: 7.33
Rank on gene expression program of genes in gene set:

Mesenchymal cells (Jansky)
Mentioned in the main text (Jansky et al, Nature Genetics (2021)), page 1, that COL1A1+ Mesenchymal were identified in their fetal adrenal glands, this is also highlighted in the UMAP plot on their Fig 1B. Additional genes also shown in their Extended data Figure 2D.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.54e-03
Mean rank of genes in gene set: 642.67
Rank on gene expression program of genes in gene set:

EMT II (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers, this EMT program was enriched in HNSCC cell lines:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.71e-03
Mean rank of genes in gene set: 1572.25
Rank on gene expression program of genes in gene set:

Hepatocytes (Jansky)
Mentioned in the main text (Jansky et al, Nature Genetics (2021)), page 1, that ALB+ Hepatocytes were identified in their fetal adrenal glands, this is also highlighted in the UMAP plot on their Fig 1B. Additional genes also shown in their Extended data Figure 2D. The main text also speculated that these hepatocytes were probably derived from neighboring tissue, and hence artifactual, but there is no evidence presented for this.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.31e-02
Mean rank of genes in gene set: 1880
Rank on gene expression program of genes in gene set:

Mesemchymal validated (Olsen)
Stated on pages 7 and 8 of the main text of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - it is stated that a mesenchymal-like neuroblastoma cell state is validate by combined immunofluorescence staining for PDGFRA and FISH for PPMID gain, a gene on 17q.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.48e-02
Mean rank of genes in gene set: 125
Rank on gene expression program of genes in gene set:

Mixed phenotype identified at the fate split point mouse (olsen)
Stated on page 6 of the main text of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - seems to be referencing previous mouse lineage tracing studies in mouse which sucggested SCPs give rise to autonomic neurons and mesenchymal cells. markers are of the split point where SCPs differentiate.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.78e-02
Mean rank of genes in gene set: 239
Rank on gene expression program of genes in gene set:

Mesenchymal (Kildisiute)
Mesenchymal markers obtained from Kildisiute et al, Supplmenentary Table 2, references supporting these genes are provided in Supp Table S2 of Kildisiute et al (PMID 33547074) https://www.science.org/doi/suppl/10.1126/sciadv.abd3311/suppl_file/abd3311_tables_s1_to_s12.xlsx:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.81e-02
Mean rank of genes in gene set: 248
Rank on gene expression program of genes in gene set:

Endothelium (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for the broad Endothelium cluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.99e-02
Mean rank of genes in gene set: 313
Rank on gene expression program of genes in gene set:

Inflammatory Macrophages (Yuan)
Obtained from Fig. 6 of Yuan et al. https://www.biorxiv.org/content/10.1101/2020.05.15.097469v1:
Wilcoxon ranksum test P-value for gene set overrepresentation: 6.36e-02
Mean rank of genes in gene set: 750
Rank on gene expression program of genes in gene set:

EMT I melanoma (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers, this EMT program was melanoma specific.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.42e-02
Mean rank of genes in gene set: 3394.67
Rank on gene expression program of genes in gene set:

SCPs mouse unique (Olsen)
Selected list of SCP marker genes shown in Fig. 2B of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - these genes were unique to mouse SCPs as determined by the linearge tracing study Furlan et al. (Science 2017, PMID 28684471).:
Wilcoxon ranksum test P-value for gene set overrepresentation: 9.55e-02
Mean rank of genes in gene set: 3906.25
Rank on gene expression program of genes in gene set:

Liver Primordium (Kameneva)
Marker gene were obtained from Fig. 1D of Kameneva et al (PMID 33833454). These genes were used by the authors to annotate each cell type in their human fetal adrenal scRNA-seq data obtained 6, 8, 9, 11, 12 and 14 weeks post conception.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.03e-01
Mean rank of genes in gene set: 3042.5
Rank on gene expression program of genes in gene set:

p53 Dependent Senescence (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.08e-01
Mean rank of genes in gene set: 3106.5
Rank on gene expression program of genes in gene set:

Pigmentation (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers, Skin pigmentation genes, identified in melanoma.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.21e-01
Mean rank of genes in gene set: 4154
Rank on gene expression program of genes in gene set:

Melanocytes (Kameneva)
Marker gene were obtained from Fig. 1D of Kameneva et al (PMID 33833454). These genes were used by the authors to annotate each cell type in their human fetal adrenal scRNA-seq data obtained 6, 8, 9, 11, 12 and 14 weeks post conception.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.34e-01
Mean rank of genes in gene set: 3959.33
Rank on gene expression program of genes in gene set:

Stromal 1 (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for Stroma subcluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.60e-01
Mean rank of genes in gene set: 4912.57
Rank on gene expression program of genes in gene set:

Schwann cell Precursor (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for the SCP subcluster, which is part of the Adrenal Medulla cluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.64e-01
Mean rank of genes in gene set: 5206.82
Rank on gene expression program of genes in gene set:

Endothelial subclusters 2-6 (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for Various endothelial subclusters of Endothelium clusters:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.83e-01
Mean rank of genes in gene set: 5544.45
Rank on gene expression program of genes in gene set:

Stromal 3 (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for Stroma subcluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.91e-01
Mean rank of genes in gene set: 4444
Rank on gene expression program of genes in gene set:

Protein maturation (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.44e-01
Mean rank of genes in gene set: 4827.33
Rank on gene expression program of genes in gene set:

Bridge (Jansky Fig1E)
Heatmap in Fig. 1E, marker genes derived from Jansks scRNA-seq data for adrenal medulla cell types.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.51e-01
Mean rank of genes in gene set: 4870
Rank on gene expression program of genes in gene set:

Endothelial Cells (Yuan)
Obtained from Fig. 6 of Yuan et al. https://www.biorxiv.org/content/10.1101/2020.05.15.097469v1:
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.74e-01
Mean rank of genes in gene set: 4733
Rank on gene expression program of genes in gene set:

Definitive Zone (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for the Definitive Zone subcluster, which is part of the Cortex cluster.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.05e-01
Mean rank of genes in gene set: 5348.75
Rank on gene expression program of genes in gene set:

Myofibroblasts (Jansky)
Mentioned in the main text (Jansky et al, Nature Genetics (2021)), page 1, that ACTA2+ Myofibroblasts were identified in their fetal adrenal glands, this is also highlighted in the UMAP plot on their Fig 1B. Additional genes also shown in their Extended data Figure 2D.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.08e-01
Mean rank of genes in gene set: 5223
Rank on gene expression program of genes in gene set:

Pre-E Chromafin (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for the Pre Epinepherine Chromaffin subcluster, which is part of the Adrenal Medulla cluster.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.08e-01
Mean rank of genes in gene set: 5749.67
Rank on gene expression program of genes in gene set:

Mesencchymal populations mouse (Olsen)
Stated on page 6 of the main text of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - seems to be referencing previous mouse lineage tracing studies in mouse which sucggested SCPs give rise to autonomic neurons and mesenchymal cells:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.13e-01
Mean rank of genes in gene set: 5026.5
Rank on gene expression program of genes in gene set:

Muscle progenitor (Jansky)
Mentioned in the main text (Jansky et al, Nature Genetics (2021)), page 1, that PAX7+ Muscle progenitor were identified in their fetal adrenal glands, this is also highlighted in the UMAP plot on their Fig 1B. Additional genes also shown in their Extended data Figure 2D.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.71e-01
Mean rank of genes in gene set: 5432.5
Rank on gene expression program of genes in gene set:

Endothelium (Kameneva)
Marker gene were obtained from Fig. 1D of Kameneva et al (PMID 33833454). These genes were used by the authors to annotate each cell type in their human fetal adrenal scRNA-seq data obtained 6, 8, 9, 11, 12 and 14 weeks post conception.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.73e-01
Mean rank of genes in gene set: 6154.25
Rank on gene expression program of genes in gene set:

EpiSen (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers, an epithelial senescence associated program.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.78e-01
Mean rank of genes in gene set: 6174.5
Rank on gene expression program of genes in gene set:

EMT III (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers, this EMT program was enriched in non-cycling cells.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.82e-01
Mean rank of genes in gene set: 6195
Rank on gene expression program of genes in gene set:

Erythroid cells (Kameneva)
Marker gene were obtained from Fig. 1D of Kameneva et al (PMID 33833454). These genes were used by the authors to annotate each cell type in their human fetal adrenal scRNA-seq data obtained 6, 8, 9, 11, 12 and 14 weeks post conception.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.91e-01
Mean rank of genes in gene set: 6190
Rank on gene expression program of genes in gene set:

Erythrocytes (Jansky)
Mentioned in the main text (Jansky et al, Nature Genetics (2021)), page 1, that HBA2+ Erythrocytes were identified in their fetal adrenal glands, this is also highlighted in the UMAP plot on their Fig 1B. Additional genes also shown in their Extended data Figure 2D.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.00e-01
Mean rank of genes in gene set: 6272
Rank on gene expression program of genes in gene set:

SCPs neuroblastoma unique (Olsen)
Similar to above, but for genes unique to neuroblastoma SCP-like cells. Note FN1 is often used as a mesenchymal marker gene.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.56e-01
Mean rank of genes in gene set: 6482.5
Rank on gene expression program of genes in gene set:

Adrenal cortex (Kildisiute)
Adrenal cortex markers obtained from Kildisiute et al, Supplmenentary Table 2, references supporting these genes are provided in Supp Table S2 of Kildisiute et al (PMID 33547074) https://www.science.org/doi/suppl/10.1126/sciadv.abd3311/suppl_file/abd3311_tables_s1_to_s12.xlsx:
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.87e-01
Mean rank of genes in gene set: 7067
Rank on gene expression program of genes in gene set:

Adrenal gland cortex (Kameneva)
Marker gene were obtained from Fig. 1D of Kameneva et al (PMID 33833454). These genes were used by the authors to annotate each cell type in their human fetal adrenal scRNA-seq data obtained 6, 8, 9, 11, 12 and 14 weeks post conception. :
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.87e-01
Mean rank of genes in gene set: 7067
Rank on gene expression program of genes in gene set:

Axon guidance (Olsen)
Markers listed in on page 4 of the main text of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - these markers are for axon guidance instead of myelination:
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.93e-01
Mean rank of genes in gene set: 7128
Rank on gene expression program of genes in gene set:

Endothelial cells (Jansky)
Mentioned in the main text (Jansky et al, Nature Genetics (2021)), page 1, that PTPRB+ Endothelial cells were identified in their fetal adrenal glands, this is also highlighted in the UMAP plot on their Fig 1B. Additional genes also shown in their Extended data Figure 2D.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 6.25e-01
Mean rank of genes in gene set: 6939
Rank on gene expression program of genes in gene set:

Bridge (Kildisiute)
Bridge cell (cites Furlan 2017) markers obtained from Kildisiute et al, Supplmenentary Table 2, references supporting these genes are provided in Supp Table S2 of Kildisiute et al (PMID 33547074) https://www.science.org/doi/suppl/10.1126/sciadv.abd3311/suppl_file/abd3311_tables_s1_to_s12.xlsx.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 6.37e-01
Mean rank of genes in gene set: 7540
Rank on gene expression program of genes in gene set:

IFN Response (Kinker)
These marker genes were obtained in a pan cancer cell lines NMF analysis of scRNA-eq data in Kinker et al (PMID 33128048) - 10 metaprograms were recovered that manifest across cancers, this program contained interferon response genes.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 6.77e-01
Mean rank of genes in gene set: 7018.2
Rank on gene expression program of genes in gene set:

Myocytes (Jansky)
Mentioned in the main text (Jansky et al, Nature Genetics (2021)), page 1, that MYH3+ Myocytes were identified in their fetal adrenal glands, this is also highlighted in the UMAP plot on their Fig 1B. Additional genes also shown in their Extended data Figure 2D.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 7.09e-01
Mean rank of genes in gene set: 7683.5
Rank on gene expression program of genes in gene set:

Bridge region mesenchymal-SCP transition (Olsen)
As above but for cells in the mesenchymal transitioning to SCP region:
Wilcoxon ranksum test P-value for gene set overrepresentation: 7.33e-01
Mean rank of genes in gene set: 7576.33
Rank on gene expression program of genes in gene set:

Myelination (Olsen)
Markers listed in on page 4 of the main text of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - these markers are state as being involved in Myelination and are expressed in the Schwann cell precursor cluster of their UMAP (Fig. 1D), these are suggested to represent more mature myelinating Schwann cells. MPZ is Myelin Protien Zero.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 7.69e-01
Mean rank of genes in gene set: 8155.5
Rank on gene expression program of genes in gene set:

PMN-MDSC
These marker genes were curated for MDSC subtypes as reviewed in Veglia et. al. (PMID 33526920):
Wilcoxon ranksum test P-value for gene set overrepresentation: 7.69e-01
Mean rank of genes in gene set: 6940.75
Rank on gene expression program of genes in gene set: